data_Y65
# 
_chem_comp.id                                    Y65 
_chem_comp.name                                  "(2~{S})-3-[1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]imidazol-4-yl]-2-azanyl-propanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H30 N8 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-21 
_chem_comp.pdbx_modified_date                    2025-04-11 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        696.455 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y65 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
Y65 C01 C1  C 0 1 N N R N N N ? ? ? -5.223  -0.043 1.979  C01 Y65 1  
Y65 C02 C2  C 0 1 N N R N N N ? ? ? -5.747  -1.188 2.883  C02 Y65 2  
Y65 C03 C3  C 0 1 N N S N N N ? ? ? -4.432  -1.847 3.367  C03 Y65 3  
Y65 C04 C4  C 0 1 N N R N N N ? ? ? -3.385  -1.408 2.325  C04 Y65 4  
Y65 C16 C5  C 0 1 N N N N N N ? ? ? 4.020   -1.742 -2.211 C16 Y65 5  
Y65 C18 C6  C 0 1 N N S N N N ? ? ? 6.071   -0.415 -2.849 C18 Y65 6  
Y65 O05 O1  O 0 1 N N N N N N ? ? ? -4.070  -0.625 1.334  O05 Y65 7  
Y65 O21 O2  O 0 1 N N N N N N ? ? ? 4.942   0.038  -0.817 O21 Y65 8  
Y65 C06 C7  C 0 1 N N N N N N ? ? ? -2.754  -2.640 1.671  C06 Y65 9  
Y65 C17 C8  C 0 1 N N R N N N ? ? ? 4.680   -0.362 -2.179 C17 Y65 10 
Y65 C19 C9  C 0 1 N N R N N N ? ? ? 6.936   0.537  -1.994 C19 Y65 11 
Y65 C20 C10 C 0 1 N N R N N N ? ? ? 5.966   1.053  -0.909 C20 Y65 12 
Y65 C23 C11 C 0 1 Y N N N N N ? ? ? 6.752   0.245  1.349  C23 Y65 13 
Y65 C25 C12 C 0 1 Y N N N N N ? ? ? 7.840   1.971  2.083  C25 Y65 14 
Y65 C26 C13 C 0 1 Y N N N N N ? ? ? 8.590   2.939  2.773  C26 Y65 15 
Y65 C28 C14 C 0 1 Y N N N N N ? ? ? 8.306   4.379  0.991  C28 Y65 16 
Y65 C30 C15 C 0 1 Y N N N N N ? ? ? 7.343   2.300  0.810  C30 Y65 17 
Y65 C37 C16 C 0 1 Y N N N N N ? ? ? -6.504  -0.311 -0.167 C37 Y65 18 
Y65 C39 C17 C 0 1 Y N N N N N ? ? ? -7.832  1.386  -0.058 C39 Y65 19 
Y65 C40 C18 C 0 1 Y N N N N N ? ? ? -7.079  1.408  1.059  C40 Y65 20 
Y65 C41 C19 C 0 1 N N N N N N ? ? ? -8.906  2.379  -0.422 C41 Y65 21 
Y65 C42 C20 C 0 1 N N S N N N ? ? ? -8.612  2.963  -1.805 C42 Y65 22 
Y65 C44 C21 C 0 1 N N N N N N ? ? ? -9.748  3.862  -2.222 C44 Y65 23 
Y65 N22 N1  N 0 1 Y N N N N N ? ? ? 6.662   1.192  0.373  N22 Y65 24 
Y65 N24 N2  N 0 1 Y N N N N N ? ? ? 7.443   0.704  2.352  N24 Y65 25 
Y65 N27 N3  N 0 1 Y N N N N N ? ? ? 8.793   4.116  2.190  N27 Y65 26 
Y65 N29 N4  N 0 1 Y N N N N N ? ? ? 7.598   3.504  0.309  N29 Y65 27 
Y65 N31 N5  N 0 1 N N N N N N ? ? ? 9.104   2.673  4.030  N31 Y65 28 
Y65 N36 N6  N 0 1 Y N N N N N ? ? ? -6.233  0.335  0.988  N36 Y65 29 
Y65 N38 N7  N 0 1 Y N N N N N ? ? ? -7.461  0.323  -0.787 N38 Y65 30 
Y65 N43 N8  N 0 1 N N N N N N ? ? ? -7.366  3.740  -1.755 N43 Y65 31 
Y65 O07 O3  O 0 1 N N N N N N ? ? ? -1.705  -2.228 0.793  O07 Y65 32 
Y65 O09 O4  O 0 1 N N N N N N ? ? ? -1.761  -4.010 -1.138 O09 Y65 33 
Y65 O10 O5  O 0 1 N N N N N N ? ? ? -0.218  -4.267 0.842  O10 Y65 34 
Y65 O11 O6  O 0 1 N N N N N N ? ? ? 0.346   -2.467 -0.835 O11 Y65 35 
Y65 O13 O7  O 0 1 N N N N N N ? ? ? 2.362   -3.985 -0.801 O13 Y65 36 
Y65 O14 O8  O 0 1 N N N N N N ? ? ? 1.353   -3.456 -3.053 O14 Y65 37 
Y65 O15 O9  O 0 1 N N N N N N ? ? ? 2.692   -1.647 -1.694 O15 Y65 38 
Y65 O32 O10 O 0 1 N N N N N N ? ? ? 7.422   1.621  -2.788 O32 Y65 39 
Y65 O33 O11 O 0 1 N N N N N N ? ? ? 5.995   0.052  -4.198 O33 Y65 40 
Y65 O34 O12 O 0 1 N N N N N N ? ? ? -4.079  -1.365 4.665  O34 Y65 41 
Y65 O35 O13 O 0 1 N N N N N N ? ? ? -6.491  -0.666 3.986  O35 Y65 42 
Y65 O45 O14 O 0 1 N N N N N N ? ? ? -9.644  5.060  -2.106 O45 Y65 43 
Y65 O46 O15 O 0 1 N N N N N N ? ? ? -10.875 3.331  -2.722 O46 Y65 44 
Y65 P08 P1  P 0 1 N N N N N N ? ? ? -0.821  -3.265 -0.065 P08 Y65 45 
Y65 P12 P2  P 0 1 N N N N N N ? ? ? 1.702   -2.912 -1.579 P12 Y65 46 
Y65 H1  H1  H 0 1 N N N N N N ? ? ? -4.932  0.818  2.580  H1  Y65 47 
Y65 H2  H2  H 0 1 N N N N N N ? ? ? -6.348  -1.893 2.309  H2  Y65 48 
Y65 H3  H3  H 0 1 N N N N N N ? ? ? -4.531  -2.933 3.375  H3  Y65 49 
Y65 H4  H4  H 0 1 N N N N N N ? ? ? -2.612  -0.808 2.806  H4  Y65 50 
Y65 H5  H5  H 0 1 N N N N N N ? ? ? 3.984   -2.104 -3.239 H5  Y65 51 
Y65 H6  H6  H 0 1 N N N N N N ? ? ? 4.599   -2.436 -1.602 H6  Y65 52 
Y65 H7  H7  H 0 1 N N N N N N ? ? ? 6.473   -1.428 -2.819 H7  Y65 53 
Y65 H8  H8  H 0 1 N N N N N N ? ? ? -2.347  -3.293 2.443  H8  Y65 54 
Y65 H9  H9  H 0 1 N N N N N N ? ? ? -3.513  -3.178 1.103  H9  Y65 55 
Y65 H10 H10 H 0 1 N N N N N N ? ? ? 4.047   0.372  -2.678 H10 Y65 56 
Y65 H11 H11 H 0 1 N N N N N N ? ? ? 7.765   -0.006 -1.539 H11 Y65 57 
Y65 H12 H12 H 0 1 N N N N N N ? ? ? 5.531   2.005  -1.211 H12 Y65 58 
Y65 H13 H13 H 0 1 N N N N N N ? ? ? 6.310   -0.739 1.300  H13 Y65 59 
Y65 H14 H14 H 0 1 N N N N N N ? ? ? 8.495   5.348  0.554  H14 Y65 60 
Y65 H15 H15 H 0 1 N N N N N N ? ? ? -6.007  -1.202 -0.521 H15 Y65 61 
Y65 H16 H16 H 0 1 N N N N N N ? ? ? -7.129  2.137  1.855  H16 Y65 62 
Y65 H17 H17 H 0 1 N N N N N N ? ? ? -9.873  1.878  -0.437 H17 Y65 63 
Y65 H18 H18 H 0 1 N N N N N N ? ? ? -8.923  3.181  0.315  H18 Y65 64 
Y65 H19 H19 H 0 1 N N N N N N ? ? ? -8.506  2.153  -2.527 H19 Y65 65 
Y65 H20 H20 H 0 1 N N N N N N ? ? ? 8.948   1.810  4.445  H20 Y65 66 
Y65 H21 H21 H 0 1 N N N N N N ? ? ? 9.620   3.349  4.496  H21 Y65 67 
Y65 H22 H22 H 0 1 N N N N N N ? ? ? -7.439  4.497  -1.092 H22 Y65 68 
Y65 H23 H23 H 0 1 N N N N N N ? ? ? -6.579  3.146  -1.540 H23 Y65 69 
Y65 H25 H25 H 0 1 N N N N N N ? ? ? -2.190  -3.414 -1.767 H25 Y65 70 
Y65 H26 H26 H 0 1 N N N N N N ? ? ? 0.918   -2.804 -3.620 H26 Y65 71 
Y65 H27 H27 H 0 1 N N N N N N ? ? ? 7.988   1.348  -3.523 H27 Y65 72 
Y65 H28 H28 H 0 1 N N N N N N ? ? ? 6.851   0.096  -4.647 H28 Y65 73 
Y65 H29 H29 H 0 1 N N N N N N ? ? ? -4.733  -1.563 5.349  H29 Y65 74 
Y65 H30 H30 H 0 1 N N N N N N ? ? ? -6.840  -1.344 4.581  H30 Y65 75 
Y65 H31 H31 H 0 1 N N N N N N ? ? ? -11.575 3.948  -2.975 H31 Y65 76 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
Y65 N43 C42 SING N N 1  
Y65 C42 C44 SING N N 2  
Y65 C42 C41 SING N N 3  
Y65 C44 O45 DOUB N N 4  
Y65 C44 O46 SING N N 5  
Y65 C41 C39 SING N N 6  
Y65 C39 N38 SING Y N 7  
Y65 C39 C40 DOUB Y N 8  
Y65 N38 C37 DOUB Y N 9  
Y65 C40 N36 SING Y N 10 
Y65 O35 C02 SING N N 11 
Y65 C37 N36 SING Y N 12 
Y65 N36 C01 SING N N 13 
Y65 C01 C02 SING N N 14 
Y65 C01 O05 SING N N 15 
Y65 C02 C03 SING N N 16 
Y65 O34 C03 SING N N 17 
Y65 O05 C04 SING N N 18 
Y65 C03 C04 SING N N 19 
Y65 C04 C06 SING N N 20 
Y65 C06 O07 SING N N 21 
Y65 O07 P08 SING N N 22 
Y65 P08 O10 DOUB N N 23 
Y65 P08 O11 SING N N 24 
Y65 P08 O09 SING N N 25 
Y65 O13 P12 DOUB N N 26 
Y65 O14 P12 SING N N 27 
Y65 O11 P12 SING N N 28 
Y65 P12 O15 SING N N 29 
Y65 O15 C16 SING N N 30 
Y65 C16 C17 SING N N 31 
Y65 C17 C18 SING N N 32 
Y65 C17 O21 SING N N 33 
Y65 C23 N24 DOUB Y N 34 
Y65 C23 N22 SING Y N 35 
Y65 C18 C19 SING N N 36 
Y65 C18 O33 SING N N 37 
Y65 N24 C25 SING Y N 38 
Y65 C19 C20 SING N N 39 
Y65 C19 O32 SING N N 40 
Y65 O21 C20 SING N N 41 
Y65 N31 C26 SING N N 42 
Y65 N22 C20 SING N N 43 
Y65 N22 C30 SING Y N 44 
Y65 C25 C26 DOUB Y N 45 
Y65 C25 C30 SING Y N 46 
Y65 C26 N27 SING Y N 47 
Y65 C30 N29 DOUB Y N 48 
Y65 N27 C28 DOUB Y N 49 
Y65 N29 C28 SING Y N 50 
Y65 C01 H1  SING N N 51 
Y65 C02 H2  SING N N 52 
Y65 C03 H3  SING N N 53 
Y65 C04 H4  SING N N 54 
Y65 C16 H5  SING N N 55 
Y65 C16 H6  SING N N 56 
Y65 C18 H7  SING N N 57 
Y65 C06 H8  SING N N 58 
Y65 C06 H9  SING N N 59 
Y65 C17 H10 SING N N 60 
Y65 C19 H11 SING N N 61 
Y65 C20 H12 SING N N 62 
Y65 C23 H13 SING N N 63 
Y65 C28 H14 SING N N 64 
Y65 C37 H15 SING N N 65 
Y65 C40 H16 SING N N 66 
Y65 C41 H17 SING N N 67 
Y65 C41 H18 SING N N 68 
Y65 C42 H19 SING N N 69 
Y65 N31 H20 SING N N 70 
Y65 N31 H21 SING N N 71 
Y65 N43 H22 SING N N 72 
Y65 N43 H23 SING N N 73 
Y65 O09 H25 SING N N 74 
Y65 O14 H26 SING N N 75 
Y65 O32 H27 SING N N 76 
Y65 O33 H28 SING N N 77 
Y65 O34 H29 SING N N 78 
Y65 O35 H30 SING N N 79 
Y65 O46 H31 SING N N 80 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
Y65 InChI            InChI                1.06  "InChI=1S/C21H30N8O15P2/c22-9(21(34)35)1-8-2-28(6-26-8)19-15(32)13(30)10(42-19)3-40-45(36,37)44-46(38,39)41-4-11-14(31)16(33)20(43-11)29-7-27-12-17(23)24-5-25-18(12)29/h2,5-7,9-11,13-16,19-20,30-33H,1,3-4,22H2,(H,34,35)(H,36,37)(H,38,39)(H2,23,24,25)/t9-,10+,11+,13+,14+,15+,16+,19+,20+/m0/s1" 
Y65 InChIKey         InChI                1.06  NPNIPERJQFLOGA-KQRTYHPUSA-N                                                                                                                                                                                                                                                                           
Y65 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](Cc1cn(cn1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O)C(O)=O"                                                                                                                                                                     
Y65 SMILES           CACTVS               3.385 "N[CH](Cc1cn(cn1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O)C(O)=O"                                                                                                                                                                                  
Y65 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(ncn1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C[C@@H](C(=O)O)N"                                                                                                                                                                      
Y65 SMILES           "OpenEye OEToolkits" 2.0.7 "c1c(ncn1C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)CC(C(=O)O)N"                                                                                                                                                                                                               
# 
_pdbx_chem_comp_identifier.comp_id           Y65 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-3-[1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]imidazol-4-yl]-2-azanyl-propanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y65 "Create component"   2023-11-21 PDBE 
Y65 "Modify coordinates" 2025-04-08 RCSB 
Y65 "Initial release"    2025-04-16 RCSB 
# 
